chr5-94630544-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032290.4(SLF1):āc.232A>Gā(p.Lys78Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,551,510 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_032290.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLF1 | NM_032290.4 | c.232A>G | p.Lys78Glu | missense_variant | 4/21 | ENST00000265140.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLF1 | ENST00000265140.10 | c.232A>G | p.Lys78Glu | missense_variant | 4/21 | 2 | NM_032290.4 | P1 | |
SLF1 | ENST00000504099.5 | c.232A>G | p.Lys78Glu | missense_variant | 5/5 | 4 | |||
SLF1 | ENST00000508130.5 | c.232A>G | p.Lys78Glu | missense_variant, NMD_transcript_variant | 4/8 | 2 | |||
SLF1 | ENST00000466957.1 | c.163A>G | p.Lys55Glu | missense_variant, NMD_transcript_variant | 3/6 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152244Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000641 AC: 1AN: 156028Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 82688
GnomAD4 exome AF: 0.0000172 AC: 24AN: 1399266Hom.: 0 Cov.: 30 AF XY: 0.0000159 AC XY: 11AN XY: 690128
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152244Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74390
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 24, 2023 | The c.232A>G (p.K78E) alteration is located in exon 4 (coding exon 3) of the SLF1 gene. This alteration results from a A to G substitution at nucleotide position 232, causing the lysine (K) at amino acid position 78 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at